GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Bacillus altitudinis 41KF2b

Align phosphate acetyltransferase; EC 2.3.1.8 (characterized)
to candidate WP_035702808.1 BA79_RS11095 phosphate butyryltransferase

Query= CharProtDB::CH_090885
         (294 letters)



>NCBI__GCF_000691145.1:WP_035702808.1
          Length = 297

 Score =  237 bits (605), Expect = 2e-67
 Identities = 124/287 (43%), Positives = 187/287 (65%), Gaps = 3/287 (1%)

Query: 6   LVEMARGKGKKLAVAAANDDHVIEAVYRAWRERVCEPVLFGPEEEITRIIE--ELVPEWK 63
           +++ ++ + K  AVA A D+ V+ A+  A   +V   +L G +  +  +++  E+  +W 
Sbjct: 7   IIKASQLQNKTAAVAHAEDEEVLHAIKMAIERKVARFLLVGNKRNLKELVKQHEINEDWI 66

Query: 64  NPQIIDCPPEEAGRLAVEAVSKGECDFLMKGKIKTGDLMKIYLDERYGLRTGKTMAMVSV 123
           +    D P EE+ ++AV+AVS+   D LMKG + T  L+K  L++ YGLRT   ++ V+ 
Sbjct: 67  DIIHSDSP-EESAKIAVQAVSENHADILMKGHVPTAILLKAVLNKEYGLRTASVLSHVAA 125

Query: 124 MEIPDFPRPLIISDPGMLISPTLEQKVDMIEHCVRVANVMGLETPKVAVVGAIEVVNPKM 183
            E+P F R + ++D  M I+P L    ++  + V+VA  +G + PKVAV+ A+EVVNP M
Sbjct: 126 FEVPGFDRFIYVTDSAMNIAPDLNMLKEITVNSVQVAQAVGNDMPKVAVLSAVEVVNPAM 185

Query: 184 PITMEAAILSKMNQRGQIKGCIVDGPFALDNVVSEEAAKKKGIQSPVAGKADILILPDIE 243
             T+ AA L++MN+RGQI GC++DGP ALDN +S+ AA  K I S VAG ADIL++P IE
Sbjct: 186 DSTLTAASLAQMNRRGQISGCLIDGPLALDNAISQTAASHKNITSDVAGHADILLVPTIE 245

Query: 244 AANILYKALVFLAKAKSASTILGGKVPVVLTSRADSEETKFYSIALS 290
           A NILYK+L++ A AK  + + G K P+ LTSR+DS E+K YSIAL+
Sbjct: 246 AGNILYKSLIYFAHAKVGAVVAGAKAPIALTSRSDSAESKLYSIALA 292


Lambda     K      H
   0.319    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 190
Number of extensions: 6
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 294
Length of database: 297
Length adjustment: 26
Effective length of query: 268
Effective length of database: 271
Effective search space:    72628
Effective search space used:    72628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory